Hi Sarah, If you just want to compare rows between two files without interpreting genome positional information (similar to the unix "comm" command), then please see the tools under "Join, Subtract and Group". In particular, "Subtract Whole Dataset", but perhaps also "Compare two Datasets". You will likely need to convert the datatype to be "tabular" before using the "Compare" function. Do this by using the "Edit Attributes -> Change data type" form, located by click on the pencil icon in the top right corner of a dataset's box in the history panel. The instructions in the "Compare" tool form state to use "Text Manipulation->Convert", but if your file is already in interval format, a specific type of tabular data, then this is not an appropriate (or needed) step. Hopefully this helps! Best, Jen Galaxy team On 10/28/11 8:19 AM, Sarah wrote:

Hi All,

I have two files containing multiple scaffolds and their genomic intervals. Now I want to substract the intervals of one file from the other, but apparently this tool is only available if all the data in the chromosome column have the same name.

Does anybody known a way how to handle files with different names in the chromosome column?

Thanks a lot in advance,

Sarah

___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:

http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists, please use the interface at:

http://lists.bx.psu.edu/

-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support